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Review
. 2014 Mar 18:5:51.
doi: 10.3389/fgene.2014.00051. eCollection 2014.

Copy number variation analysis in the context of electronic medical records and large-scale genomics consortium efforts

John J Connolly  1 , Joseph T Glessner  2 , Berta Almoguera  1 , David R Crosslin  3 , Gail P Jarvik  3 , Patrick M Sleiman  2 , Hakon Hakonarson  2
Affiliations
Review

Copy number variation analysis in the context of electronic medical records and large-scale genomics consortium efforts

John J Connolly et al. Front Genet. .

Abstract

The goal of this paper is to review recent research on copy number variations (CNVs) and their association with complex and rare diseases. In the latter part of this paper, we focus on how large biorepositories such as the electronic medical record and genomics (eMERGE) consortium may be best leveraged to systematically mine for potentially pathogenic CNVs, and we end with a discussion of how such variants might be reported back for inclusion in electronic medical records as part of medical history.

Keywords: CNV; copy number; eMERGE; review; structural variation.

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Figures

FIGURE 1
FIGURE 1
CNV detection using different platforms: platforms vary in their capacities to detect CNVs.
FIGURE 2
FIGURE 2
CNV detection in SNP-array data using PennCNV: example log R ratio (LRR) and B Allele Freq (BAF) values for the chromosome 15 q-arm of an individual. Three normal chromosomal BAF genotype clusters (AA, AB, and BB genotypes) have LRR values around zero. The copy-neutral loss-of-heterozygosity (LOH) region has normal LRR values, but no AB cluster. Increased copy number can be observed in the increased number of peaks in the BAF distribution and increased LRR values. LRR and BAF patterns are different for different CNV regions, and can be used to generate CNV calls. Adapted from Wang et al. (2007).
See this image and copyright information in PMC

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